IQ-TREE multicore version 1.6.11 for Linux 64-bit built Jun  6 2019
Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor,
Heiko Schmidt, Dominik Schrempf, Michael Woodhams.

Host:    rabi (SSE4.2, 15 GB RAM)
Command: ../../iqtree -s Troglosironidae_3genes.raxml -sp Troglosironidae_4genes.partitions.txt -pre Troglosironidae_3genes.raxml -m TEST -bb 1000 -alrt 1000
Seed:    520499 (Using SPRNG - Scalable Parallel Random Number Generator)
Time:    Tue Nov 19 03:23:19 2019
Kernel:  SSE2 - 1 threads (24 CPU cores detected)

HINT: Use -nt option to specify number of threads because your CPU has 24 cores!
HINT: -nt AUTO will automatically determine the best number of threads to use.

Reading partition model file Troglosironidae_4genes.partitions.txt ...
Reading alignment file Troglosironidae_3genes.raxml ... Phylip format detected
Alignment most likely contains DNA/RNA sequences
Alignment has 31 sequences with 4943 columns, 1003 distinct patterns
561 parsimony-informative, 327 singleton sites, 4055 constant sites
                               Gap/Ambiguity  Composition  p-value
   1  H_tama_IZ134691                  2.55%    passed     30.53%
   2  M_savannahensis_IZ134557         2.53%    passed      5.41%
   3  O_cameroonensis_IZ132315         2.97%    failed      0.01%
   4  P_gabonica_IZ132297              2.31%    failed      1.29%
   5  T_aelleni_IZ134764               0.20%    passed     97.85%
   6  T_cf_platnicki_IZ134766          0.45%    passed     96.48%
   7  T_dogny_IZ151570_1              16.37%    failed      3.57%
   8  T_dogny_IZ151570_2              16.37%    failed      3.57%
   9  T_juberthiei_IZ134763f           2.49%    passed     98.62%
  10  T_juberthiei_IZ134763m           1.05%    passed     97.73%
  11  T_juberthiei_IZ134767_1          3.36%    passed     61.65%
  12  T_longifossa_IZ65208             0.28%    passed     95.24%
  13  T_monteithi_IZ51948              4.77%    passed     98.32%
  14  T_ninqua_IZ134768                0.77%    passed     98.10%
  15  T_oscitatio_IZ72572             10.52%    failed      1.05%
  16  T_pin_IZ133854_1                 0.99%    passed     99.74%
  17  T_pseudojuberthiei_IZ133855_1    0.55%    passed     98.24%
  18  T_pseudojuberthiei_IZ133856      0.59%    passed     98.38%
  19  T_pseudojuberthiei_IZ133857_2    1.19%    passed     99.46%
  20  T_pseudojuberthiei_IZ133859_2   47.58%    passed     11.39%
  21  T_pseudojuberthiei_IZ133870_1   44.24%    failed      0.00%
  22  T_pseudojuberthiei_IZ133870_5   62.65%    failed      0.00%
  23  T_pseudojuberthiei_IZ151618_1   16.33%    failed      3.27%
  24  T_pseudojuberthiei_IZ151618_2   16.33%    failed      3.84%
  25  T_raveni_IZ134777               23.04%    failed      0.04%
  26  T_sharmai_IZ151558_1            16.67%    passed      7.64%
  27  T_sharmai_IZ151558_2            16.31%    failed      4.66%
  28  T_sheari_IZ72565                17.70%    failed      0.79%
  29  T_urbanus_IZ134780f             16.14%    passed      8.61%
  30  T_urbanus_IZ134780m              3.97%    passed     97.84%
  31  T_wilsoni_IZ134787               1.66%    passed     64.33%
WARNING: 1 sequences contain more than 50% gaps/ambiguity
****  TOTAL                           11.38%  12 sequences failed composition chi2 test (p-value<5%; df=3)

Partition file is not in NEXUS format, assuming RAxML-style partition file...
Subset	Type	Seqs	Sites	Infor	Invar	Model	Name
1	DNA	27	462	168	223	GTR	16S
2	DNA	31	1761	13	1701	GTR	18S
3	DNA	29	2063	103	1816	GTR	28S
4	DNA	30	657	277	315	GTR	COI
Degree of missing data: 0.043
Info: multi-threading strategy over partitions

NOTE: T_dogny_IZ151570_2 is identical to T_dogny_IZ151570_1 but kept for subsequent analysis


Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.007 seconds
NOTE: ModelFinder requires 7 MB RAM!
Testing GTR+F+G on supermatrix...
GTR+F+G4 / LnL: -17431.455 / df: 68 / AIC: 34998.910 / AICc: 35000.835 / BIC: 35441.300
Selecting individual models for 4 charsets using BIC...
 No. Model        Score       Charset
   1 TIM2+F+G4    6052.897    16S
   2 TNe+I        6321.077    18S
   3 TVM+F+I      10084.804   28S
   4 TIM+F+I+G4   11631.535   COI
Full partition model BIC score: 34477.995 (LnL: -16184.287  df:248)
Partition information was printed to Troglosironidae_3genes.raxml.best_scheme.nex
Partition information in Raxml format was printed to Troglosironidae_3genes.raxml.best_scheme

All model information printed to Troglosironidae_3genes.raxml.model.gz
CPU time for ModelFinder: 17.294 seconds (0h:0m:17s)
Wall-clock time for ModelFinder: 17.608 seconds (0h:0m:17s)
Generating 1000 samples for ultrafast bootstrap (seed: 520499)...

NOTE: 6 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
Optimizing TIM+F+I+G4 parameters for partition COI (65 free parameters)
Optimizing TVM+F+I parameters for partition 28S (63 free parameters)
Optimizing TIM2+F+G4 parameters for partition 16S (58 free parameters)
Optimizing TNe+I parameters for partition 18S (62 free parameters)
Optimal log-likelihood: -16183.908
Computing ML distances based on estimated model parameters... 0.022 sec
Computing BIONJ tree...
0.053 seconds
Log-likelihood of BIONJ tree: -16219.106
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.698 second
Computing log-likelihood of 98 initial trees ... 2.190 seconds
Current best score: -16183.908

Do NNI search on 20 best initial trees
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -16170.582
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -16170.542
Iteration 10 / LogL: -16170.547 / Time: 0h:0m:10s
Iteration 20 / LogL: -16170.547 / Time: 0h:0m:12s
Finish initializing candidate tree set (2)
Current best tree score: -16170.542 / CPU time: 7.671
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 25: -16166.361
UPDATE BEST LOG-LIKELIHOOD: -16166.361
Iteration 30 / LogL: -16173.533 / Time: 0h:0m:15s (0h:0m:52s left)
UPDATE BEST LOG-LIKELIHOOD: -16166.360
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 35: -16165.623
Iteration 40 / LogL: -16168.115 / Time: 0h:0m:19s (0h:0m:47s left)
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 44: -16165.380
Iteration 50 / LogL: -16166.459 / Time: 0h:0m:22s (0h:0m:43s left)
Log-likelihood cutoff on original alignment: -16203.184
BETTER TREE FOUND at iteration 58: -16165.370
Iteration 60 / LogL: -16171.108 / Time: 0h:0m:25s (0h:0m:42s left)
Iteration 70 / LogL: -16166.001 / Time: 0h:0m:28s (0h:0m:36s left)
Iteration 80 / LogL: -16166.398 / Time: 0h:0m:31s (0h:0m:30s left)
Iteration 90 / LogL: -16170.793 / Time: 0h:0m:34s (0h:0m:26s left)
Iteration 100 / LogL: -16171.315 / Time: 0h:0m:36s (0h:0m:21s left)
Log-likelihood cutoff on original alignment: -16198.626
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.996
UPDATE BEST LOG-LIKELIHOOD: -16165.369
Iteration 110 / LogL: -16165.605 / Time: 0h:0m:39s (0h:0m:32s left)
UPDATE BEST LOG-LIKELIHOOD: -16165.365
Iteration 120 / LogL: -16165.976 / Time: 0h:0m:43s (0h:0m:28s left)
Iteration 130 / LogL: -16165.975 / Time: 0h:0m:46s (0h:0m:24s left)
Iteration 140 / LogL: -16165.385 / Time: 0h:0m:48s (0h:0m:21s left)
Iteration 150 / LogL: -16165.382 / Time: 0h:0m:51s (0h:0m:17s left)
Log-likelihood cutoff on original alignment: -16198.626
UPDATE BEST LOG-LIKELIHOOD: -16165.363
TREE SEARCH COMPLETED AFTER 159 ITERATIONS / Time: 0h:0m:54s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
Optimizing TIM+F+I+G4 parameters for partition COI (65 free parameters)
Optimizing TVM+F+I parameters for partition 28S (63 free parameters)
Optimizing TIM2+F+G4 parameters for partition 16S (58 free parameters)
Optimizing TNe+I parameters for partition 18S (62 free parameters)
Optimal log-likelihood: -16165.349
BEST SCORE FOUND : -16165.349

Testing tree branches by SH-like aLRT with 1000 replicates...
1.883 sec.
Creating bootstrap support values...
Split supports printed to NEXUS file Troglosironidae_3genes.raxml.splits.nex
Total tree length: 1.555

Total number of iterations: 159
CPU time used for tree search: 48.993 sec (0h:0m:48s)
Wall-clock time used for tree search: 49.764 sec (0h:0m:49s)
Total CPU time used: 55.623 sec (0h:0m:55s)
Total wall-clock time used: 56.608 sec (0h:0m:56s)

Computing bootstrap consensus tree...
Reading input file Troglosironidae_3genes.raxml.splits.nex...
31 taxa and 192 splits.
Consensus tree written to Troglosironidae_3genes.raxml.contree
Reading input trees file Troglosironidae_3genes.raxml.contree
Log-likelihood of consensus tree: -16165.585

Analysis results written to: 
  IQ-TREE report:                Troglosironidae_3genes.raxml.iqtree
  Maximum-likelihood tree:       Troglosironidae_3genes.raxml.treefile
  Likelihood distances:          Troglosironidae_3genes.raxml.mldist
  Best partitioning scheme:      Troglosironidae_3genes.raxml.best_scheme.nex
           in RAxML format:      Troglosironidae_3genes.raxml.best_scheme

Ultrafast bootstrap approximation results written to:
  Split support values:          Troglosironidae_3genes.raxml.splits.nex
  Consensus tree:                Troglosironidae_3genes.raxml.contree
  Screen log file:               Troglosironidae_3genes.raxml.log

Date and Time: Tue Nov 19 03:24:34 2019
